Math371 Course Material

Math 371 - Fall 2017

Project-related papers

* Tyson, Chen & Novak - "Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell" - Current Opinion in Cell Biology (2003)

Warming up projects

* Guantes & Poyatos - "Dynamical principles of two-component genetic oscillators" - PLoS Computational Biology (2006)

Design 1 (K. C. & R. P)
Design 2 (A. P. & K. Mu.)

* Novak & Tyson - "Design principles of biochemical oscillators" - Nature Reviews Molecular Biology (2008)

Negative feedback with time delay model (A. A. & S. F.)
Time delay by a series of intermediates (M. J. & A. O.)
Time delay by positive feedback (A. D. & B. W.)
Biochemical interaction networks: delayed negative feedback loops (X. Z. & Y. M.)
Amplified negative feedback loops (G. T. & S. N.)
Incoherently amplified negative-feedback loops (D. D. & K. Ma.)

* Gonzalez, Markadieu & Gonze - "Selection of in-phase or out-of-phase syncrhonization in a model based on global coupling of cells undergoing metabolic oscillations" - Chaos (2008)

Single oscillator model (P. V. & S. K.)

* Woller, Gonze & Erneux - "The Goodwin model revisited: Hopf bifurcation, limit-cycle, and periodic entrainment" - Phys Biol (2014)

Single oscillator model (A. O. & K. M.)

* Tyson - "Biochemical Oscillations" - Chapter 9

Substrate-depletion oscillator (B. E. & Z. M.)
Activator-inhibitor oscillator (R. E.)
The Goodwin oscillator
Circadian rhythms (M-P) model

.

Recommended Reading and Matlab Codes

Matlab Tutorial (Kohitij Kar)

Matlab Tutorial
Solutions

ODE Examples (modified Euler method, Matlab)

Logistic growth with threshold equation
Linear ODE order 2

Enzymatic reactions: competitive and allosteric inhibition: Matlab codes (RJ Leiser) for the presentations by O. Flodin, E. Khan, R. J. Leiser, K. Niknam.

Allosteric Inhibition
Competitive Inhibition
Competitive and Allosteric Inhibition

Dynamics of cell regulation and biological oscillations

Tyson, Chen & Novak - "Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell" - Current Opinion in Cell Biology (2003)
Novak & Tyson - "Design principles of biochemical oscillators" - Nature Reviews Molecular Biology (2008)
Competitive and Allosteric Inhibition

.
.
.
.
.
.
.
.
. Department of Mathematical Sciences(DMS).
New Jersey Institute of Technology (NJIT).

Horacio
Last modified: Thu Sep 2 10:45:36 EDT 2017